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Department of Pediatrics, Division of Infectious Diseases, and Departments of 2Laboratory Medicine and 3Epidemiology and Public Health,
Yale University School of Medicine, New Haven, Connecticut
(See the brief report by Esper et al., on pages 499502, and the editorial commentary by McIntosh, on pages 48991.)
Received 7 September 2004; accepted 8 November 2004; electronically published 14 January 2005.
Financial support: Patrick and Catherine Weldon Donaghue Medical Research
Foundation (to J.S.K.); Friends of Yale Pediatrics (to J.S.K.); Yale Childrens Clinical
Research Center (grant M01-RR06022 to J.S.K.); General Clinical Research Centers
Program, National Center for Research Resources, National Institutes of Health
(NIH); NIH (grant T32 AI07210-20 to F.E.).
Reprints or correspondence: Dr. Jeffrey S. Kahn, Dept. of Pediatrics, Div. of
Infectious Diseases, Yale University School of Medicine, P.O. Box 208064, New
Haven, CT 06520-8064 (jeffrey.kahn@yale.edu).
The Journal of Infectious Diseases 2005; 191:4928
2005 by the Infectious Diseases Society of America. All rights reserved.
0022-1899/2005/19104-0002$15.00
Background. The etiological agents responsible for a substantial proportion of respiratory tract diseases have
not been identified. We sought to determine whether novel human coronaviruses (HCoVs) are circulating in New
Haven, Connecticut, and, if so, whether they are associated with respiratory tract disease in infants and young
children.
Methods. We developed a polymerase chain reaction (PCR)based approach for screening specimens from
the respiratory tracts of symptomatic children. PCR probes that target regions of the replicase 1a gene that are
conserved among genetically diverse animal CoVs and HCoVs were designed. Using these probes, we identified
genomic sequences of a novel HCoV, designated New Haven coronavirus (HCoV-NH). Thereafter, we designed
specific probes to screen respiratory specimens from children !5 years old for this novel HCoV. Clinical features
associated with HCoV-NH infection were identified.
Results. Seventy-nine (8.8%) of 895 children tested positive for HCoV-NH. Cough, rhinorrhea, tachypnea,
fever, abnormal breath sounds, and hypoxia were the most common findings associated with HCoV-NH infection.
Sequence analysis revealed that HCoV-NH is closely related to a novel HCoV recently reported in The Netherlands.
Conclusions. The novel HCoVs identified in New Haven and The Netherlands are similar and likely represent
the same species. This newly discovered virus may have worldwide distribution and may account for a significant
proportion of respiratory tract disease in infants and young children.
tionarily maintained by all CoVs. Therefore, we designed polymerase chain reaction (PCR) probes that target regions of the
CoV replicase 1a gene that are conserved among HCoVs, avian
CoVs, and mammalian CoVs. Using this approach, we identified genetic evidence of a novel HCoV circulating in New
Haven, CT. Probes specific for this HCoV, designated New
Haven coronavirus (HCoV-NH), were then used to screen
specimens from the respiratory tracts of symptomatic children.
During our screening of respiratory specimens for this HCoV,
2 studies from The Netherlands reported the identification of
a novel HCoV [10, 11]. This virus is a group 1 CoV and is
most closely related to HCoV-229E and transmissible gastroenteritis virus (TGEV), a virus of pigs. Comparisons of the
sequences of the HCoV identified in The Netherlands and
HCoV-NH revealed that these viruses are closely related and
likely represent the same species. Here, we describe the seasonal distribution and clinical manifestation of disease associated
with HCoV-NH infection.
Figure 1. Age distribution of New Haven coronavirus (HCoV-NH)positive children !5 years old. HCoV-NH infection in children hospitalized since
birth at the newborn intensive care unit (NICU), YaleNew Haven Hospital (CT), is represented by black bars.
Table 1. Clinical features associated with New Haven coronavirus infection in children !5
years old.
Clinical feature
Cough
Rhinorrhea
Tachypneaa
Feverb
Rhonchi, rales, or abnormal breath sounds
Hypoxiac
Chest retractions
Wheezing
Stridor
Abnormal chest-radiograph findingsd
NOTE.
a
b
c
(0)
(27.3)
(81.8)
(18.2)
(54.5)
(81.8)
(27.3)
(9.1)
(0)
(71.4)
43
38
30
30
24
16
19
20
4
20/31
(76.8)
(67.9)
(53.6)
(53.6)
(42.9)
(28.6)
(33.9)
(35.7)
(7.1)
(64.5)
43
41
39
32
30
25
22
21
4
25/38
(64.2)
(61.2)
(58.2)
(47.8)
(44.8)
(37.3)
(32.8)
(31.3)
(6.0)
(65.8)
Data are no. (%) of children, except where noted. NICU, newborn intensive care unit.
0
3
9
2
6
9
3
1
0
5/7
Total
(n p 67)
spiratory secretions from individuals with SARS, broadly reactive PCR was used to identify the pathogen; unlike in the
present study, in which the replicase 1a gene was targeted, the
replicase 1b gene was targeted in the identification of the agent
that causes SARS [5].
In the present study, the initial set of primers, used to screen
pooled specimens, were less sensitive than the HCoV-NHspecific primers. Many of the respiratory specimens in the initial pool of 601 specimens that tested negative by PCR with
the replicase 1a gene primers tested positive by PCR with the
HCoV-NHspecific primers. Subsequent sequence analysis of
the target sites for the replicase 1a gene of HCoV-NH (data
not shown) revealed several mismatches between the genome
and primer sequence. This finding likely accounts for the relative decreased sensitivity of the replicase 1a gene primers.
Among the 601 specimens initially screened, the 2 pooled reactions that tested positive for HCoV-NH contained multiple
positive specimens. This may account for why these pooled
specimens tested positive. It is also unclear why primers constructed for the detection of the 2 common HCoVs, HCoV229E and HCoV-OC43, would not have detected HCoV-NH.
Presumably, the genomic sequence targeted for the detection
of HCoV-229E and HCoV-OC43 is specific for these viruses.
The sensitivity of the CoV consensus primers and the HCoVNHspecific primers is unknown. Determination of the sensitivity will require propagation of the virus and development
of a method for quantitating the number of viral particles (such
as an infectivity assay or a method based on electron microscopy, neither of which have been completely developed for
496 JID 2005:191 (15 February) Esper et al.
HCoV-NH). As further genetic data become available, moresensitive primers may be developed.
Our approach complements that of traditional virology, in
which viruses are identified by their effects on cells in tissue
culture. However, the identification of previously unknown viruses on the basis of in vitro findings has significant shortcomings, not the least of which is the inability to amplify and
characterize unique genetic sequences. This obstacle was overcome by Fouchier et al. [10] and van der Hoek et al. [11], who
used the tools of molecular biology to identify and sequence
the genome of a novel HCoV in The Netherlands after propagation in cell culture. hMPV was discovered by use of a similar approach that was based on in vitro virus propagation
and genomic amplification techniques [15]. Like the 2 groups
from The Netherlands, we have evidence that this novel HCoV
can be propagated in cell culture. The results of RT-PCR assays
of passaged cell culture supernatants suggested the growth of
HCoV-NH in vitro (data not shown).
There were early hints that HCoV-229E and HCoV-OC43 were
not the only common HCoVs. The first HCoV isolated, B814,
was not serologically related to either HCoV-229E or HCoVOC43 [16]. McIntosh et al. demonstrated that 3 of the 6 OC
strains isolated from adults with colds appeared to be serologically unrelated, or at least distantly related, to HCoV-OC43 and
HCoV-229E [17]. Experimental infection of human volunteers
with these 6 OC strains confirmed this finding [18]. It was,
therefore, unlikely that HCoV-229E and HCoV-OC43 were the
only HCoVs. The viral pathogen newly identified in New Haven
Figure 2. Weekly distribution of New Haven coronavirus (HCoV-NH)positive children !5 years old from January 2002 to mid-February 2003. For
clarity, only the first day of every other week is labeled. HCoV-NH infection in children hospitalized since birth at the newborn intensive care unit
(NICU), YaleNew Haven Hospital (CT), is represented by black bars.
Children
148
117
123
74
48
19
42
29
38
89
137
144
99
81
98
51
32
15
17
19
22
61
105
104
8
27
8
3
4
4
0
5
4
0
0
4
177
80
1265
129
62
895
4 (3.1)
8 (12.9)
79 (8.8)
(8.1)
(33.3)
(8.2)
(5.9)
(12.5)
(26.7)
(0)
(26.3)
(18.2)
(0)
(0)
(3.8)
and The Netherlands may represent the first of many antigenically distinct groups of HCoVs to be characterized.
In the present study, HCoV-NH was associated with both
upper and lower respiratory tract disease in infants and young
children. Because ours was not a population-based study and
because a control group was not included, it is impossible to
determine the spectrum of disease caused by HCoV-NH infection. Our study screened specimens submitted to a diagnostic laboratory only; therefore, the proportion of children
with clinical illness reported here likely does not reflect that of
the general population. Likewise, the issue of causality remains
unresolved. Prospective population-based studies are required.
Nonetheless, the identification of genetic sequences of this HCoV
Figure 3. Phylogenetic analysis of New Haven coronavirus (HCoV-NH). To construct the phylogenetic tree, sequences of a 126-bp portion of the
replicase 1a gene of a representative sample of HCoV-NH (NH) amplicons, the HCoV recently identified in The Netherlands (NL-63), HCoV-229E, and
transmissible gastroenteritis virus (TGEV) were used.
Novel Human Coronavirus JID 2005:191 (15 February) 497
2002
January
February
March
April
May
June
July
August
September
October
November
December
2003
January
February
Total
Specimens
Acknowledgments
We are indebted to George Miller, John F. Enders Professor of Pediatric
Infectious Diseases (Yale University School of Medicine), for his continued
support, intellectual and scientific input and exchange, and critical review
of the data and manuscript. We thank the staff of the Clinical Virology
Laboratory, YaleNew Haven Hospital (CT), for their assistance. We are
also indebted to Eugene D. Shapiro (Yale University School of Medicine),
for his thoughtful review of the manuscript.
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